Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate WP_090447263.1 BLS63_RS18495 dicarboxylate/amino acid:cation symporter
Query= TCDB::Q01857 (444 letters) >NCBI__GCF_900100495.1:WP_090447263.1 Length = 417 Score = 255 bits (652), Expect = 2e-72 Identities = 143/401 (35%), Positives = 226/401 (56%), Gaps = 13/401 (3%) Query: 22 LYVQVLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFLTVATGIAGMSDLQ 81 L+ Q+LV +A G+ G + + L P+G F+ +KM+I P++F+++ GI M D Sbjct: 17 LWQQILVGLALGVATGLAFEQDAQVLAPVGALFLNAIKMLIVPLVFVSLVAGITAMQDSA 76 Query: 82 KVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVATFAAKAHEQ- 140 K+GR++ K + +L + A+ IGL+ + PG GM + VA+ ++A + Sbjct: 77 KLGRISAKTIAIYLVTTAFAVSIGLLFGTLFTPGEGMQM---------VASAGSEAKQAP 127 Query: 141 SIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQVVNFLNSLTAPVFK 200 S+ G L ++P+ + AFA+G+ILQ++ F++ G+++ +VG K VV +SL ++K Sbjct: 128 SLAGILVGLVPSNPISAFAEGNILQIIVFAIALGVSMNLVGAKAAPVVKLFDSLAEVLYK 187 Query: 201 LVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLLFVFIVLGA-VARYNG 259 L ++M+ AP G F +A +G +G + LA +IG Y+ L V +V G + + Sbjct: 188 LTDLIMRLAPYGVFALIAGVVGSHGAEVLLPLAGVIGVIYLACLAHVLLVYGGLIGLFAR 247 Query: 260 FSIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEK-AGCKRSVVGLVIPTGYSFNLDGT 318 + + L+ I L + TSSS LP + K G V G V+P G + N+DGT Sbjct: 248 LNPLRFLQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGT 307 Query: 319 NIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFITLAATLSVVPSVP 378 IY + ALFIAQA GI LS G ++++L A L+S G AG+ GAG I L L+ V +P Sbjct: 308 AIYQGVLALFIAQAFGIELSGGQYLMIILTATLASIGTAGVPGAGLIMLGLVLTSV-GLP 366 Query: 379 VAGMALILGIDRFMSECRALTNLVGNAVATIVVARWENELD 419 + G+ALI GIDR + R N+ G+ + T +V R ENELD Sbjct: 367 LEGVALIAGIDRILDMARTTVNVAGDLMTTTLVGRSENELD 407 Lambda K H 0.324 0.139 0.393 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 531 Number of extensions: 34 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 444 Length of database: 417 Length adjustment: 32 Effective length of query: 412 Effective length of database: 385 Effective search space: 158620 Effective search space used: 158620 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory